Editorial

Surprisingly, only 2% of the mammalian genome encodes
proteins, whereas an estimated 98% accounts for non-coding
RNA that includes anywhere from 20,000 to 100,000 long noncoding
RNA (lncRNA) transcripts. It is now clear that many
lncRNA are indeed functional and regulate bi-directional gene
transcription. Hence, understanding the function of lncRNA
transcripts from a massive transcriptome is an utmost priority
and challenge. In a recent Leading Edge review published in
Cell (Cell 172, January 25, 2018), Joshua T. Mendall (HHMI)
and Florian Kopp from University of Texas South-western
Medical Centre, provide a conceptual and rational experimental
framework for mechanistic classification and function of
lncRNA. They categorized lncRNA based on genomic location
and mode of regulatory function (cis vs. trans).

Mechanisms of LncRNA Regulation

Regarding the cis acting mechanism of lncRNA function, the
authors discuss three mechanisms through which lncRNAs
can influence the chromatin state of nearby genes. The first
cis mechanism, sequence-dependent lncRNA regulation, is
modelled by one of the best studied mechanisms of lncRNA
regulation, Xist-mediated silencing of one X chromosome
in females, known as X chromosome inactivation (Xi).
Mechanistically, the lncRNA Xist recruits regulatory factors
to the promoters of neighboring genes and thereby regulates
promoter function. The sequence-specific requirements have
been well studied, yet some of the mechanisms involved in this
process remain debated.

In the second cis mechanism discussed, the transcription and/
or splicing of the lncRNA locus controls the transcription of
the neigh boring gene in a manner independent of the lncRNA
transcript or product. In these cases, silencing by the lncRNA
appears to be mediated by transcriptional overlap, such that
transcription of the lncRNA prevents RNA polymerase II (Pol
II) recruitment to the promoter of the neighboring gene, even
in the presence of active chromatin. Furthermore, evidence
suggests that transcription or splicing of some lncRNAs alters the chromatin state of neighboring gene promoters, thereby
regulating the expression of those genes.

Lastly, DNA elements present within an lncRNA promoter or
gene locus may function in cis, independently of the lncRNA
product, to regulate neighboring genes. Indeed, recent studies
suggest that the regulation of gene expression by enhancerlike
elements that reside within the lncRNA locus but function
independently of the lncRNA may be relatively common.

Kopp and Men dell note that lncRNAs that function in trans
can also be grouped into three categories: those that regulate
chromatin and gene expression at distant sites, those that alter
nuclear structure and organization, and those that interact with
and regulate the behavior of other proteins or RNA that regulate
transcription. These latter interactions may occur in the nucleus
or the cytoplasm.

Discerning Chaos from Function

Despite the recent attention to lncRNAs and advances in the
experimental procedures available to study these ubiquitous
RNAs, numerous confounding factors have complicated efforts
to define the functions of individual lncRNAs. For example,
the human transcripts of some lncRNAs display limited to no
sequence similarity to the respective mouse transcripts. This
raises concern about whether the associated gene-regulatory
mechanisms are the same in rodent cells and in human cells.
Moreover, lncRNAs that function in trans through direct
binding mechanisms may require stoichiometric interaction
for observable effects, thus experimental conditions must be
rigorously evaluated. Methods for reliably inhibiting lncRNAs,
especially those in the nucleus, are also needed.

Over the last decade, the regulatory functions of numerous
lncRNAs, including Xist, HOTAIR, and MALAT1, have been
well studied. On the other hand, many studies of lncRNA
have encouraged spirited debate over whether noncoding
RNAs represent “non-coding transcriptional chaos” or serve
as truly functional regulatory RNAs. Undoubtedly, there is
no definitive answer. Rigorous approaches can persuasively
identify and characterize functional lncRNAs linked to biology.

Hence, I am very hopeful that persistent research on lncRNA
epitranscriptome will keep due promise to uncover new and
unanticipated regulation to impact our fundamental basis for
normal physiology and disease.